Your post does contain the line “they remained unhappy with the broader policy of respect for trans identities”, which to me reads as being at least pretty similar to having “issue with transgender identities.” But I’m an outsider to all this and may be missing context.
Could you elaborate? Because I’m confused by what you could mean here. What is the broader policy that they disagree with? You say they “did agree with the specific neopronouns policy”, so it seems like you are saying they agree that “harassment based on gender or neopronouns [should] remain prohibited—even if the user in question was suspected of being a troll”? If the broader policy is a policy of “respect for trans identities”, it seems like the only thing about the policy they have a problem with is its respect for trans identities.